Dear all,
I am doing MD simulation studies on hemoglobin heme ligated with CO. I used charmm27 and mentioned the all bond details such as bonds between CO, HIS with heme in specbond.dat. It does recognizes the bonds and created the bonds in topology file using pdb2gmx. Moreover, I have added the heme hydrogen details in aminoacids.hdb after searching few details in gromacs user page. However, i am struct with the steps in adding the ions to the protein as it gives the errors like No default Proper Dih. types , No default U-B types No default Bond types I believe these faults are arise from the bonds which i mentioned in specbond.dat. I do have the parameter files of these heme-co ligand (literature and AMBER database) and do not know how do i interpret in here to avoid this problem? Any suggestion and advice please. Thanks all. Raju
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